1) Option in the submission/update form for dependancies. List would be pulled from the site's DB, it'd auto-generate links to the mod so the author doesn't have to track down the mod and link it in the description.
2) A setting to sort comments on a mod by newest first
3) Auto-notify via email if a comment is added to one of the mods you author. Include the comment in the email too
4) Seperate feild in the form for patch notes and known bugs. When a new version is posted include the patch notes in the email sent out to users watching the mod as a favorite.